[Chimera-users] help

Mon Jun 13 07:05:33 PDT 2011

Hello Elaine,

Can you please help in how to map this data (confidence map) in the
following attachment.
It has a fourth dimension which is the confidence.
You can open the attachment with notepad.

Regards,
Chinmaya

On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi <jchinu2014 at gmail.com>wrote:

> Dear Elaine,
>
>
> Thanks a lot for the molmap command.
>
> I want to map the x,y,z co-ordinates and the intensity of each pixel.
>
> Regards,
> Chinmaya
> On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi Chinmaya,
>> Forget the script, just use the Chimera "molmap" command.  That python
>> script may have been written before we had the command.  Now that you
>> already figured out an input format and opened it in Chimera, you only need
>> to show the command line (from Favorites menu in Chimera) and enter one
>> "molmap" command, something like
>>
>> molmap #0 15
>>
>> where the first number is the model number of the points and the second
>> number is a resolution, related to Gaussian width. You may wish to use a
>> different resolution, and there are other options, see
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
>>
>> I would have mentioned "molmap" earlier if you had said you wanted to make
>> a map from your points.
>> Elaine
>>
>> On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote:
>>
>> > Hey Elaine,
>> >
>> > Thanks for the mail.
>> >
>> > Just open the file in notepad and save it as .xyz (dont need to do that
>> I am attaching the file here now)
>> > Then I have just opened this  .xyz file  in chimera and chimera loads
>> the desired image(attached: open with notepad or any text editor)(I have
>> also attached the output image of chimera)
>> >
>> > Now my question is that
>> > How do I use the script calle xyzmap.py on the following link
>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
>> > for opening the above file from the command line.
>> > what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py
>> code with?
>> >
>> > Regards,
>> > Chinmaya
>> > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> > Hi Chinmaya,
>> > The way to see if Chimera opens your file is to either
>> > (A) look at the list of file types in the link I sent in the previous
>> message, or
>> > (B) start Chimera, and try using File... Open in the menu.
>> >
>> > However, no:  Chimera does not read a ".csv" file.  You never said what
>> your file is supposed to contain, but from the name and contents of the file
>> it appears to be x,y,z coordinates of a bunch of dots.  If you just want to
>> display this as a bunch of dots or spheres in Chimera, you could convert
>> this file (write a script to do it in any language you like) to the simple
>> "BILD" text format described here:
>> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
>> >
>> > Then the "BILD" file (name it something.bild) can be opened in Chimera
>> to display the dots or spheres.
>> >
>> > As I mentioned earlier I do not know python, and I don't recommend it in
>> this case.  Using python would require some knowledge of Chimera code.
>>  Instead use a Chimera command script.
>> >
>> > Just start Chimera, open the BILD file, show the Chimera command line
>> (choose from the Favorites menu), try typing in commands.  Figure out the
>> movement commands you want, then put the commands and movie-recording
>> commands in text file to make the Chimera script.  Command "roll" does
>> rotation, "move" does translation, "scale" does scaling, "movie" does the
>> movie stuff. The script might be as simple as:
>> >
>> > movie record
>> > roll y 1 360; wait
>> > wait 10
>> > movie stop
>> > movie encode mformat mov output /MyPath/mymovie.mov
>> >
>> > ... but you would need to look at the command documentation to see what
>> options you want.  There are links to that documentation and to example
>> Chimera command scripts in my previous message.
>> > Elaine
>> >
>> > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote:
>> >
>> > > Hello Elaine,
>> > >
>> > > Thanks a lot for your mail. I am working on the points you have
>> suggested. However I am a bit confused whether my input files will work in
>> chimera or not?
>> > > Herewith I am attaching a sample example of the  dataset which I will
>> be taking as the input, perform some viewpoint operation on it and then make
>> a movie.
>> > > Can you please let me know whether this can be done in chimera or not?
>> > > If yes, can it be done in a python script file?
>> > >
>> > > Regards,
>> > > Chinmaya Joshi
>> > >
>> > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng <meng at cgl.ucsf.edu>
>> wrote:
>> > > Hi Chinmaya,
>> > > Before you start scripting, the first thing to consider is whether
>> Chimera can do what you want.  Have you tried doing what you want to show in
>> the movie, but while using Chimera interactively?  From your description, I
>> am concerned that Chimera may not read your input format.  The input types
>> are generally 3D data files, not images.  The one exception is that an image
>> stack can be used as a "volume data" input format.  Here is information on
>> what formats Chimera can read:
>> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
>> > >
>> > > If you think Chimera can do what you want, here is information on
>> making movies,
>> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html>
>> > >
>> > > ...including commands for rotation and translation, etc.
>> > > <
>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands
>> >
>> > >
>> > > ...and example scripts
>> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples
>> >
>> > >
>> > > ...however, these examples are Chimera command scripts, not python
>> scripts. I think python scripts would be more difficult to make than Chimera
>> command scripts, and you would only start working with python if (A) Chimera
>> can do what you want or nearly so, but (B) there are no Chimera commands for
>> those things.  After you figure out what you want to do by using Chimera
>> interactively, then figure out the commands for those actions, then put them
>> into a script.  The last step would be to add movie recording commands to
>> that script.
>> > >
>> > > I don't know python, so I can't say any more about using that
>> approach.
>> > >
>> > > I hope this helps,
>> > > Elaine
>> > > -----
>> > > Elaine C. Meng, Ph.D.
>> > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> > > Department of Pharmaceutical Chemistry
>> > > University of California, San Francisco
>> > >
>> > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote:
>> > >
>> > > > Hello,
>> > > > I want to write a script in python to open a set of images in
>> chimera set a viewpoint(rotate, translate,etc). and make a movie out of them
>> all through command line for my project.
>> > > >
>> > > > Can someone please let me know how it can be done.
>> > > >
>> > > > I am new to python.
>> > > >
>> > > > Can anyone tell me any good links for these?
>> > > >
>> > > > The documentation on chimera ucsf is a bit confusing.
>> > > > Thanks.
>> > > > Chinmaya
>> > >
>> > >
>> > > <pointcloud.csv>_______________________________________________
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>> > > Chimera-users at cgl.ucsf.edu
>> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> >
>> >
>> >
>> <trial5.xyz><image_stickman2.png>_______________________________________________
>> > Chimera-users mailing list
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>>
>>
>
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